namsaraeva

namsaraeva's Stars

• cookiecutter/cookiecutter

  A cross-platform command-line utility that creates projects from cookiecutters (project templates), e.g. Python package projects, C projects.

  Language:Python23.3k2318772.1k

• napari/napari

  napari: a fast, interactive, multi-dimensional image viewer for python

  Language:Python2.3k443.2k437

• scverse/scanpy

  Single-cell analysis in Python. Scales to >100M cells.

  Language:Python2k481.8k620

• merveenoyan/my_notes

  My small cheatsheets for data science, ML, computer science and more.

  1.6k281119

• MouseLand/cellpose

  a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

  Language:Jupyter Notebook1.6k28956440

• theislab/single-cell-best-practices

  https://www.sc-best-practices.org

  Language:Jupyter Notebook86817210206

• scverse/anndata

  Annotated data.

  Language:Python61312766161

• theislab/ehrapy

  Electronic Health Record Analysis with Python.

  Language:Python281434524

• scverse/spatialdata

  An open and interoperable data framework for spatial omics data

  Language:Python2691247458

• scverse/pertpy

  Perturbation Analysis in the scverse ecosystem.

  Language:Python167626928

• cookiejar/cookietemple

  A collection of best practice cookiecutter templates for all domains and languages with extensive Github support ⛺

  Language:Python159528210

• glencoesoftware/bioformats2raw

  Bio-Formats image file format to raw format converter

  Language:Java85189435

• TissueImageAnalytics/cerberus

  One Model is All You Need: Multi-Task Learning Enables Simultaneous Histology Image Segmentation and Classification

  Language:Python8262612

• YeoLab/bento-tools

  A Python toolkit for subcellular analysis of spatial transcriptomics data

  Language:Python764877

• scverse/cookiecutter-scverse

  Cookiecutter template for scverse

  Language:Python75510211

• scverse/spatialdata-io

  Language:Python55612233

• EliHei2/segger_dev

  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).

  Language:Python541435

• JacobHanimann/scDINO

  Self-Supervised Vision Transformers for multiplexed imaging datasets

  Language:Python494610

• scverse/spatialdata-plot

  Static plotting for spatialdata

  Language:Python49820916

• MannLabs/scPortrait

  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images

  Language:Python4241173

• MannLabs/alphabase

  Infrastructure of AlphaX ecosystem

  Language:Jupyter Notebook378469

• manzt/napari-lazy-openslide

  Lazily load multiscale whole-slide images with openslide and dask

  Language:Python33157

• scverse/conference-2024

  Slides and Notebooks for scverse 2024

  Language:Jupyter Notebook17301

• MannLabs/SPARCSpy

  Language:Jupyter Notebook112176

• RTH-tools/CRISPRsummerschool

  Language:Jupyter Notebook9201

• theislab/ehrapy-datasets

  A collection of scripts to generate AnnData objects of EHR datasets for ehrapy

  Language:Jupyter Notebook7212

• spyysalo/dl-binf-summer-school-2024

  Material for 2024 Summer School on Applied Deep Learning in Bioinformatics

  Language:Jupyter Notebook6102

• kaspergl/ML23

  Machine Learning 2023

  Language:Jupyter Notebook311

• MannLabs/scPortrait-notebooks

  Language:Jupyter Notebook210